Arabidopsis_clock_P2011 - PLM_64

This model is termed P2011 and derives from the article: <strong>The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops</strong><strong>. </strong>Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday &amp; Andrew J Millar <em>Mol. Syst. Biol. </em>2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. <a href="http://www.nature.com/msb/journal/v8/n1/synopsis/msb20126.html">Link</a>   Link to <a href="http://www.nature.com/msb/journal/v8/n1/extref/msb20126-s1.pdf">Supplementary Information</a>, including equations. Minor errors in the published Supplementary Information are described in a file attached to version 1 of this model (the published SBML is correct).    The model describes the circuit depicted in Fig. 1 of the paper (GIF attached). It updates the Pokhilko et al. 2010 model (termed P2010), <a href="http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_6">PLM_6</a>, by including:<ol>

  • the Evening Complex genes (ELF4, ELF3, LUX),
  • light-regulated degradation of ELF3 by COP1,
  • TOC1 as a repressor rather than an activator of LHY/CCA1.
  • These changes allowed the removal of hypothetical components TOC1mod (or X) and Y from the earlier models. They also reveal that the central loop of the model is a triple-repressor ring oscillator, or 'repressilator' (illustrated in Fig. 8, GIF attached). SBML curation notes (please see Comments for each version): Compared to the model version submitted to the Biomodels database, version 1 here slightly alters the names of some variables and uses an SBML AssignmentRule for the light input. A MATLAB version is attached to version 1. In version 2, the rule is used with a generic SBML StepFunction (Adams et al. J. Biol. Rhythms Aug 2012) to describe the light-dark cycle more flexibly. Versions 1 and 2 have multiple sinks and sources created by CellDesigner. These are removed in versions 3 & 4. Version 3 has the published lightfunction, and an equivalent COPASI file attached. Version 4 has the StepFunction.

    Related Publications
    Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar (2012). The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops.. Mol. Syst. Biol. 8: 574.. Retrieved from: http://www.nature.com/msb/journal/v8/n1/synopsis/msb20126.html

    Originally submitted to PLaSMo on 2012-03-07 12:15:12

    Help
    help Creators and Submitter
    Creators
    Submitter
    Activity

    Views: 1514

    Created: 10th Jan 2019 at 17:38

    Last updated: 22nd Jan 2019 at 18:17

    Related items

    Powered by
    (v.1.11.3)
    Copyright © 2008 - 2021 The University of Manchester and HITS gGmbH

    By continuing to use this site you agree to the use of cookies